RetrogeneDB ID: retro_mmus_2721

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 6:18824551..18825055(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000071568
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Tsen15
• Ensembl ID: ENSMUSG00000014980
• Aliases: Tsen15, 5730449L18Rik, AL023077, Sen15
• Description: tRNA splicing endonuclease 15 homolog (S. cerevisiae) [Source:MGI Symbol;Acc:MGI:1913887]

Sequence

>retro_mmus_2721
ATGGAGGAGCACAGCGATTCCGAACCTACCCCGGGATGTAGCGGGCCTGGCCTGGCTCCCGTTCGCGATGGCGGCGGCGC
CCACACATGGGCTCCGGAGGACGCCTGGATGGGCACACACCCTAAGTACTTAGAAATGATGGAATTAGATATAGGAGATG
CCACCCAAGTTTATATAGCATTCTTGGTTTACCTGGATCTCATGGAGAGTAAAAGTTGGCATGAAGTAAACTGTGTAGGA
ATACCAGAACTACAACTCATCTGCCTCCTTGGCACTGAGATCGAAGGGGAAGGGCTGCAGACAGTGGTGCCTACACCCAT
TTCTGCTTCCCTCAGCCATAATAGGATAAGGGAAATCTTGAAGGCGTCTAGAAAGTTGCAAGGCGATCCAGAACTGCCAA
TGTCTTTTACTTTGGCCATAGTGGAGTCAGATTCCACAATAGTCTATTATAAACTTACCGATGGATTTATGCTGCCAGAC
CCTCAGAATATTTCTCTTAGAAGA

Alignment

ORF - retro_mmus_2721 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.21 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MEERSDSKPTPGCSGPGPAPVRDGGGAHTWAPEDAWMGTHPKYLEMMELDIGDATQVYIAFLVYLDLMES
          MEE.SDS.PTPGCSGPG.APVRDGGGAHTWAPEDAWMGTHPKYLEMMELDIGDATQVYIAFLVYLDLMES
Retrocopy MEEHSDSEPTPGCSGPGLAPVRDGGGAHTWAPEDAWMGTHPKYLEMMELDIGDATQVYIAFLVYLDLMES

Parental  KSWHEVNCVGIPELQLICLLGTEIEGEGLQTVVPTPISASLSHNRIREILKASRKLQGDPELPMSFTLAI
          KSWHEVNCVGIPELQLICLLGTEIEGEGLQTVVPTPISASLSHNRIREILKASRKLQGDPELPMSFTLAI
Retrocopy KSWHEVNCVGIPELQLICLLGTEIEGEGLQTVVPTPISASLSHNRIREILKASRKLQGDPELPMSFTLAI

Parental  VESDSTIVYYKLTDGFMLPDPQNISLRR
          VESDSTIVYYKLTDGFMLPDPQNISLRR
Retrocopy VESDSTIVYYKLTDGFMLPDPQNISLRR

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP007412_brain	0.02 RPM	8.11 RPM
SRP007412_cerebellum	0.35 RPM	8.38 RPM
SRP007412_heart	0.00 RPM	5.29 RPM
SRP007412_kidney	0.35 RPM	4.77 RPM
SRP007412_liver	0.08 RPM	1.83 RPM
SRP007412_testis	0.09 RPM	2.79 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_2721 was not detected

EST

No EST(s) were mapped for retro_mmus_2721 retrocopy.

TSS

No TSS is located nearby retro_mmus_2721 retrocopy 5' end.

Lab

retro_mmus_2721 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2721 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000016369	1 retrocopy	retro_btau_971,
Callithrix jacchus	ENSCJAG00000005356	1 retrocopy	retro_cjac_3055,
Dasypus novemcinctus	ENSDNOG00000017611	2 retrocopies	retro_dnov_1176, retro_dnov_2529,
Homo sapiens	ENSG00000198860	1 retrocopy	retro_hsap_1721,
Gorilla gorilla	ENSGGOG00000015804	2 retrocopies	retro_ggor_2267, retro_ggor_240,
Loxodonta africana	ENSLAFG00000014109	1 retrocopy	retro_lafr_684,
Macaca mulatta	ENSMMUG00000016409	1 retrocopy	retro_mmul_1214,
Mustela putorius furo	ENSMPUG00000011790	1 retrocopy	retro_mputfur_1261,
Mus musculus	ENSMUSG00000014980	1 retrocopy	retro_mmus_2721 ,
Nomascus leucogenys	ENSNLEG00000018024	1 retrocopy	retro_nleu_98,
Otolemur garnettii	ENSOGAG00000003128	1 retrocopy	retro_ogar_3264,
Pongo abelii	ENSPPYG00000000421	4 retrocopies	retro_pabe_1436, retro_pabe_3065, retro_pabe_3196, retro_pabe_469,
Pan troglodytes	ENSPTRG00000023202	2 retrocopies	retro_ptro_1229, retro_ptro_147,
Pteropus vampyrus	ENSPVAG00000001103	1 retrocopy	retro_pvam_1458,
Ictidomys tridecemlineatus	ENSSTOG00000013230	2 retrocopies	retro_itri_1538, retro_itri_1849,
Vicugna pacos	ENSVPAG00000002941	2 retrocopies	retro_vpac_381, retro_vpac_565,